Another update after a few workdays with my i7 SP3.
I am now 99% sure that the thermal throttling has nothing to do with the hardware or the airflow and is all in the drivers with the graphics chip. Today I compressed a 30GB virtual machine using 7zip and using all 4 logical cores. It took over an hour with the processor pegged between 93 and 100% load. Throughout the whole hour, not once did the surface drop below 2.1GHz, mostly sitting around 2.2GHz at 80 degrees Celsius. The surface pro 3 is perfectly capable of maintaining high speeds and acceptable temperatures for long periods of time, I have only observed throttling when something graphical (aka a video game) is also in play, using the Intel graphics 5000 as well. I will try to run some sort of graphical stress test to confirm this, but from a compression stress test, purely processor, the surface performs perfectly.